Multi-target list of B0FieldIdentifier entities skips SDC

[miltoncamacho]

What happened?

SDC workflow is skipped regardless of the B0FieldIdentifiers being properly defined and --use-syn-sdc error being used.

What command did you use?

export FMRIPREP_COMPUTE_OPTIONS="--omp-nthreads 8 --nprocs 12 --mem_mb 32000"
export FMRIPREP_OUTPUT_SPACES="--output-spaces MNI152NLin2009cAsym T1w:res-iso2mm"
export FMRIPREP_PIPELINE_OPTIONS="--output-layout bids --dummy-scans 0 --ignore slicetiming --use-syn-sdc error --me-output-echos"

sudo docker run --rm \
-v ${bids_dir}:/outputs/bids \
-v ${fmriprep_report}:/outputs/fmriprep-report \
-v ${fmriprep_work_folder}:/outputs/fmriprep-work \
-v ${fresurfer_license}:/opt/freesurfer/license.txt:ro \
nipreps/fmriprep:latest /outputs/bids /outputs/fmriprep-report participant \
--skip-bids-validation \
--participant-label ${subjects} \
--stop-on-first-crash --debug all \
--me-t2s-fit-method loglin \
-w /outputs/fmriprep-work \
--fs-license-file /opt/freesurfer/license.txt \
${FMRIPREP_COMPUTE_OPTIONS} \
${FMRIPREP_OUTPUT_SPACES} \
${FMRIPREP_PIPELINE_OPTIONS}

What version of fMRIPrep are you running?

25.1.3

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

Work directory

Please copy and paste any relevant log output.

Running fMRIPrep version 25.1.3

         License NOTICE ##################################################
         fMRIPrep 25.1.3
         Copyright The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250715-17:19:10,723 nipype.workflow IMPORTANT:
	 Building fMRIPrep's workflow:
           * BIDS dataset path: /outputs/bids.
           * Participant list: ['2532', '2928', '2976', '3136', '3328', '3398'].
           * Run identifier: 20250715-171747_dd3dc0ec-6d0b-4cd9-9152-5b2b83ba6d32.
           * Output spaces: MNI152NLin2009cAsym:res-native T1w:res-iso2mm.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /outputs/fmriprep-report/sourcedata/freesurfer.
250715-17:19:28,535 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:29,265 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:42,62 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:42,748 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:43,962 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:56,762 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:19:57,450 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:10,600 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:11,889 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:27,446 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:28,144 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:37,843 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:20:38,519 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
250715-17:21:02,165 nipype.workflow IMPORTANT:
	 fMRIPrep started!
250715-17:21:08,811 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-laluna_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:08,960 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:09,137 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-01_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:09,313 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-02_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:09,474 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:09,670 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-laluna_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:09,818 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,44 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-laluna_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,198 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,387 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-laluna_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,551 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,731 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-laluna_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:10,874 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-partlycloudy_desc-hmc_boldref.nii.gz dtype from int16 to int16
250715-17:21:16,347 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-laluna_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:16,494 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:16,730 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-01_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:16,939 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-02_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:17,225 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:17,557 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-laluna_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:17,747 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:18,8 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-laluna_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:18,186 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:18,520 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-laluna_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:18,761 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:18,998 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-laluna_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:21:19,138 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-partlycloudy_desc-coreg_boldref.nii.gz dtype from int16 to int16
250715-17:33:11,420 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-laluna_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,565 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,641 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-01_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,713 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-02_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,785 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,859 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-laluna_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,928 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:11,997 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-laluna_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:12,180 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:12,256 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-laluna_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:12,358 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:12,435 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-laluna_desc-brain_mask.nii.gz dtype from float32 to float32
250715-17:33:12,497 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-partlycloudy_desc-brain_mask.nii.gz dtype from float32 to float32
250715-20:47:35,381 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/anat/sub-2532_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250715-20:47:36,419 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/anat/sub-2532_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250715-20:48:27,860 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-laluna_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-20:48:47,313 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-21:47:39,494 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/anat/sub-2928_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250715-21:47:40,533 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/anat/sub-2928_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250715-21:48:37,320 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-01_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-21:48:58,278 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-02_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-21:49:18,304 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-22:47:55,584 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/anat/sub-2976_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250715-22:47:56,626 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/anat/sub-2976_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250715-22:48:48,591 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-laluna_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-22:49:07,783 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-23:48:42,305 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/anat/sub-3136_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250715-23:48:43,356 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/anat/sub-3136_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250715-23:49:36,388 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-laluna_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250715-23:49:56,367 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250716-00:48:36,153 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/anat/sub-3328_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-00:48:37,183 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/anat/sub-3328_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250716-00:49:28,967 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-laluna_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250716-00:49:49,430 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:47:50,923 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/anat/sub-3398_ses-1a_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:47:51,978 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/anat/sub-3398_ses-1a_space-MNI152NLin2009cAsym_dseg.nii.gz dtype from float64 to float64
250716-01:48:43,987 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-laluna_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:03,319 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-partlycloudy_space-T1w_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:16,69 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-laluna_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:16,301 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:49,796 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:50,25 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-laluna_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:49:50,254 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2928/ses-1a/func/sub-2928_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:50:23,582 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-laluna_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:50:23,814 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-2976/ses-1a/func/sub-2976_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:50:55,612 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-laluna_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:50:55,838 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3136/ses-1a/func/sub-3136_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:51:29,504 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-laluna_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:51:29,726 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3328/ses-1a/func/sub-3328_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:52:03,541 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-laluna_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:52:03,766 nipype.interface WARNING:
	 Changing /outputs/fmriprep-report/sub-3398/ses-1a/func/sub-3398_ses-1a_task-partlycloudy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz dtype from float64 to float64
250716-01:57:24,658 nipype.workflow IMPORTANT:
	 fMRIPrep finished successfully!
250716-01:57:24,659 nipype.workflow IMPORTANT:
	 Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.

Additional information / screenshots

It runs with no errors and produces the html report but SDC is not run. Here is the fmriprep.toml for the run.

[environment]
cpu_count = 112
exec_env = "docker"
free_mem = 483.6
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "24.2.2"
version = "25.1.3"

[execution]
bids_dir = "/outputs/bids"
bids_database_dir = "/outputs/fmriprep-work/20250715-171747_dd3dc0ec-6d0b-4cd9-9152-5b2b83ba6d32/bids_db"
bids_description_hash = "cebbba58753725dc994fc65c74be5585740493d33dd9ffcb5dd4275dda68fe84"
boilerplate_only = false
sloppy = false
debug = [ "compcor", "fieldmaps", "pdb",]
fmriprep_dir = "/outputs/fmriprep-report"
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/outputs/fmriprep-report/sourcedata/freesurfer"
layout = "BIDS Layout: .../outputs/bids | Subjects: 6 | Sessions: 6 | Runs: 2"
log_dir = "/outputs/fmriprep-report/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/outputs/fmriprep-report"
me_output_echos = true
aggr_ses_reports = 4
output_layout = "bids"
output_spaces = "MNI152NLin2009cAsym:res-native T1w:res-iso2mm"
reports_only = false
run_uuid = "20250715-171747_dd3dc0ec-6d0b-4cd9-9152-5b2b83ba6d32"
participant_label = [ "2532", "2928", "2976", "3136", "3328", "3398",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/outputs/fmriprep-work"
write_graph = false

[workflow]
anat_only = false
bold2anat_dof = 6
bold2anat_init = "t1w"
cifti_output = false
dummy_scans = 8
fmap_bspline = false
force_syn = false
hires = true
fs_no_resume = false
ignore = [ "slicetiming",]
force = []
level = "full"
longitudinal = false
run_msmsulc = true
medial_surface_nan = false
project_goodvoxels = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "MNI152NLin2009cAsym:res-native T1w:res-iso2mm"
use_syn_sdc = "error"
me_t2s_fit_method = "loglin"

[nipype]
crashfile_format = "txt"
get_linked_libs = false
memory_gb = 32.0
nprocs = 12
omp_nthreads = 8
plugin = "Linear"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = true

[seeds]
master = 7280
ants = 10584
numpy = 13916

[execution.derivatives]

[execution.dataset_links]
raw = "/outputs/bids"
templateflow = "/home/fmriprep/.cache/templateflow"

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

Here are some examples of the report showing that SDC was not run:

[miltoncamacho]

I am not sure if the --participant-label flag is causing this behaviour by using it or the fact that we are running multiple subjects --participant-label 123 1234 12345. I will run this with only one subject --participant-label 123 to start narrowing down the issue. Any ideas would be welcomed.

[miltoncamacho]

We are doing PEpolar SDC, B0FieldIdentifiers example:

json side car of one of the func run contains.

"B0FieldSource": "sub_3328_ses_1a_task_laluna"

json side car of one of AP fmap contains:

"B0FieldIdentifier": [
"sub_3328_ses_1a_task_laluna",
"sub_3328_ses_1a_task_partlycloudy"
],

and

"IntendedFor": [
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-1_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-2_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-3_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-4_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-1_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-2_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-3_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-4_bold.nii.gz"
],

json side car of one of PA fmap contains:

"B0FieldIdentifier": [
"sub_3328_ses_1a_task_laluna",
"sub_3328_ses_1a_task_partlycloudy"
],

and

"IntendedFor": [
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-1_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-2_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-3_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-laluna_echo-4_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-1_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-2_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-3_bold.nii.gz",
"ses-1a/func/sub-3328_ses-1a_task-partlycloudy_echo-4_bold.nii.gz"
],

[mgxd]

My guess is the problem lies with B0FieldIdentifier being a list - can you try running on a single subject after modifying the fieldmap metadata to just

"B0FieldIdentifier": "sub_3328_ses_1a_task_laluna"

[miltoncamacho]

Thanks for the reply, I have another run task_partlycloudy that also expects to use the calculated fmap, I just removed it for simplicity in the example. I have used the B0FieldIdentifier as a list in the past successfully, shouldn't this work still in version 25.1.3?

Update: I have not tested using "B0FieldIdentifier" as a list like I thought, I was using "B0FieldIdentifier": "sub_3328_ses_1a_task_laluna" for a test I ran in v 24.1.1 I will give this a try.

My question is now, is the expected behaviour to use a single B0FieldIdentifier for all the runs that need the specific fmap?

[mgxd]

We should support lists as they are valid, but I'm not seeing this being explicitly tested in sdcflows (where most of the sdc code is located) - could very well be an oversight. Though, if you are using the same files to construct the B0Field, there's no reason to create separate identifiers for each task.

[miltoncamacho]

I see, this is something that get populated from our bids conversion step, we will need to make sure it only creates a single identifier for the reverse polarity fmap pair.

[bpinsard]

The list issue was supposedly fixed in nipreps/sdcflows#298 and a pybids fix, will look into it.

[bpinsard]

Our script to fill B0 Intent can create some partial overlaps and some duplicates of estimators depending on the strategy, but is still BIDS valid.
This is an issue for sdcflows, because it was trying to guess a name for the estimators, the PR linked above fixes that by simply passing the bids_id when creating the FieldmapEstimation as it was maybe first intended.

[miltoncamacho]

Hi @mgxd sdcflows pullreq 497 has been merged which fixes this issue, when do we think this would be integrated into fmriprep?

[mgxd]

25.1.4 is available, which includes the fix - please reopen if you are still running into issues